> When did you add in the coordpdb line? Was it above or below this section?
> If atom positions aren't initialized, they will be put at the origin by
> default, which is normally not what people want. My guess is that you put
> it above the section, so that psfgen came across atoms it didn't recognize
> and ignored them, only to have you patch them in afterward with the
> coordinates placed at the origin.
> -Josh Vermaas
>
> On 12/11/2015 05:07 AM, Francesco Pietra wrote:
>
> Hello:
>
> With CHARMM36, VMD in text mode, the .gen file including:
>
> patch GLUP PRA:235
> patch ASPP PRA:516
>
> regenerate angles dihedrals
>
> (the protein pdb included all H-atoms), the log file reports that it was
> unable to read HE2 and HD2 for the above residues. The result was that
> these atoms were put outside the protein.
>
> On removing HE2 and HD2 from the pdb, no more such warnings, however,
> again, both atoms placed outside the protein. Apparently the patch was
> accepted.
> ..............................
>
> Moreover, despite the error reported in the log file;
>
> psfgen) Toplogy and parameter information for water and ions.
> psfgen)
> psfgen) ERROR! FAILED TO RECOGNIZE SET
> psfgen) ERROR! FAILED TO RECOGNIZE SET
> psfgen) ERROR! FAILED TO RECOGNIZE IF
> psfgen) ERROR! FAILED TO RECOGNIZE READ
> psfgen) Topology for water and ions
> psfgen)
> psfgen) ERROR! FAILED TO RECOGNIZE 31
> psfgen) skipping statements at end of file due to end or return statement
>
> a ligand CLA of the protein was set correctly. is there any possible
> modification of the str file, or should I extract from it the relevant
> portions in order to skip what VMD is unable to read from CHARMM36?
> ......................................
>
> Grateful for advice
>
> francesco pietra
>
>
>